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2E84
Asym. Unit
Info
Asym.Unit (109 KB)
Biol.Unit 1 (99 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIGH-MOLECULAR WEIGHT CYTOCHROME C FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F) IN THE PRESENCE OF ZINC ION
Authors
:
N. Shibata, K. Suto, M. Sato, Y. Morimoto, M. Kitamura, Y. Higuchi
Date
:
17 Jan 07 (Deposition) - 15 Jan 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Cytochrome C3 Motifs, Electron Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Osuka, K. Suto, M. Sato, N. Shibata, M. Kitamura, Y. Morimoto, K. Ozawa, H. Akutsu, Y. Higuchi, N. Yasuoka
Structure Of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F)
To Be Published
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
1e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
1f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
1g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
1h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
1i: PROTOPORPHYRIN IX CONTAINING FE (HEMi)
1j: PROTOPORPHYRIN IX CONTAINING FE (HEMj)
1k: PROTOPORPHYRIN IX CONTAINING FE (HEMk)
1l: PROTOPORPHYRIN IX CONTAINING FE (HEMl)
1m: PROTOPORPHYRIN IX CONTAINING FE (HEMm)
1n: PROTOPORPHYRIN IX CONTAINING FE (HEMn)
1o: PROTOPORPHYRIN IX CONTAINING FE (HEMo)
1p: PROTOPORPHYRIN IX CONTAINING FE (HEMp)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
16
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
NA
4
Ligand/Ion
SODIUM ION
3
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(24, 24)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:190 , LYS A:193 , GLU A:415 , ASP A:419 , GLU A:553
BINDING SITE FOR RESIDUE ZN A 557
02
AC2
SOFTWARE
HIS A:534 , GLU A:540 , GLU A:549
BINDING SITE FOR RESIDUE ZN A 558
03
AC3
SOFTWARE
LYS A:355 , GLU A:442 , HEM A:1309
BINDING SITE FOR RESIDUE ZN A 559
04
AC4
SOFTWARE
HIS A:320 , LYS A:323 , ILE A:324 , ASP A:325 , HOH A:1361
BINDING SITE FOR RESIDUE ZN A 560
05
AC5
SOFTWARE
LYS A:307 , LYS A:523 , HIS A:527 , HOH A:1409
BINDING SITE FOR RESIDUE NA A 561
06
AC6
SOFTWARE
LYS A:32 , GLU A:124 , HOH A:1494
BINDING SITE FOR RESIDUE NA A 562
07
AC7
SOFTWARE
ASP A:136 , HOH A:1513
BINDING SITE FOR RESIDUE NA A 563
08
AC8
SOFTWARE
MET A:279 , HEM A:1308 , HOH A:1319
BINDING SITE FOR RESIDUE NA A 564
09
AC9
SOFTWARE
ILE A:48 , PHE A:64 , HIS A:66 , HIS A:69 , GLU A:82 , CYS A:83 , CYS A:86 , HIS A:87 , LEU A:97 , LYS A:98 , PHE A:99 , ARG A:101 , TYR A:114 , ARG A:221 , HIS A:225 , ILE A:229 , HEM A:1307 , HOH A:1428 , HOH A:1512
BINDING SITE FOR RESIDUE HEM A 1301
10
BC1
SOFTWARE
VAL A:62 , THR A:63 , PHE A:64 , ARG A:68 , HIS A:69 , VAL A:73 , PHE A:99 , ASN A:117 , CYS A:118 , CYS A:121 , HIS A:122 , GLN A:125 , LYS A:131 , THR A:132 , GLY A:133 , HOH A:1417 , HOH A:1469
BINDING SITE FOR RESIDUE HEM A 1302
11
BC2
SOFTWARE
ILE A:48 , GLY A:49 , VAL A:50 , MET A:51 , LEU A:57 , GLU A:58 , LEU A:59 , VAL A:62 , LYS A:111 , TYR A:114 , HIS A:115 , CYS A:118 , ILE A:119 , GLN A:135 , ASP A:136 , GLU A:138 , CYS A:139 , CYS A:142 , HIS A:143
BINDING SITE FOR RESIDUE HEM A 1303
12
BC3
SOFTWARE
GLY A:156 , LEU A:157 , HIS A:162 , HIS A:165 , ASN A:180 , CYS A:181 , CYS A:184 , HIS A:185 , GLU A:202 , SER A:204 , LEU A:270 , GLU A:271 , THR A:315 , CYS A:316 , ARG A:317 , ILE A:324 , HEM A:1306 , HOH A:1333 , HOH A:1470 , HOH A:1477
BINDING SITE FOR RESIDUE HEM A 1304
13
BC4
SOFTWARE
LYS A:94 , HIS A:185 , HIS A:186 , LEU A:195 , ASP A:203 , SER A:204 , CYS A:205 , CYS A:208 , HIS A:209 , LYS A:216 , PRO A:218 , ALA A:223 , GLN A:227 , HOH A:1476
BINDING SITE FOR RESIDUE HEM A 1305
14
BC5
SOFTWARE
LEU A:161 , ARG A:164 , HIS A:165 , ILE A:171 , GLN A:227 , CYS A:228 , CYS A:231 , HIS A:232 , ASP A:243 , SER A:244 , GLY A:245 , PHE A:261 , HEM A:1304 , HOH A:1474
BINDING SITE FOR RESIDUE HEM A 1306
15
BC6
SOFTWARE
VAL A:46 , HIS A:66 , GLN A:154 , ILE A:155 , ARG A:206 , LEU A:220 , ARG A:221 , ALA A:224 , HIS A:225 , CYS A:228 , HIS A:232 , VAL A:247 , SER A:248 , CYS A:249 , CYS A:252 , HIS A:253 , HEM A:1301 , HOH A:1331 , HOH A:1503
BINDING SITE FOR RESIDUE HEM A 1307
16
BC7
SOFTWARE
ARG A:272 , GLN A:274 , PHE A:304 , HIS A:306 , HIS A:309 , SER A:313 , THR A:315 , CYS A:316 , CYS A:319 , HIS A:320 , ASP A:325 , ASN A:326 , CYS A:327 , THR A:328 , NA A:564 , HOH A:1318 , HOH A:1364
BINDING SITE FOR RESIDUE HEM A 1308
17
BC8
SOFTWARE
CYS A:319 , HIS A:320 , HIS A:321 , VAL A:322 , ASN A:326 , CYS A:327 , CYS A:330 , HIS A:331 , ASP A:338 , GLY A:339 , ASN A:340 , ALA A:347 , SER A:353 , LYS A:355 , GLU A:442 , ZN A:559 , HOH A:1452
BINDING SITE FOR RESIDUE HEM A 1309
18
BC9
SOFTWARE
VAL A:302 , PHE A:304 , ASN A:305 , HIS A:309 , MET A:354 , SER A:356 , CYS A:357 , CYS A:360 , HIS A:361 , ARG A:428 , LEU A:476 , THR A:479 , HEM A:1312
BINDING SITE FOR RESIDUE HEM A 1310
19
CC1
SOFTWARE
VAL A:365 , ALA A:369 , CYS A:370 , CYS A:373 , HIS A:374 , MET A:377 , THR A:379 , GLN A:384 , PRO A:385 , ILE A:471 , ASP A:474 , LEU A:476 , PHE A:480 , HIS A:481 , THR A:486 , VAL A:487 , ALA A:489 , GLY A:490 , HOH A:1385
BINDING SITE FOR RESIDUE HEM A 1311
20
CC2
SOFTWARE
VAL A:280 , LEU A:281 , PRO A:282 , GLY A:297 , ALA A:298 , MET A:299 , ILE A:344 , MET A:348 , HIS A:349 , CYS A:357 , HIS A:361 , GLN A:384 , ALA A:388 , CYS A:389 , CYS A:392 , HIS A:393 , HEM A:1310 , HOH A:1366
BINDING SITE FOR RESIDUE HEM A 1312
21
CC3
SOFTWARE
THR A:434 , LEU A:435 , ILE A:440 , ILE A:446 , LEU A:458 , HIS A:460 , VAL A:487 , CYS A:488 , CYS A:491 , HIS A:492 , PRO A:501 , LYS A:503 , CYS A:504 , TYR A:526 , HEM A:1315 , HOH A:1471 , HOH A:1503
BINDING SITE FOR RESIDUE HEM A 1313
22
CC4
SOFTWARE
PHE A:376 , LYS A:378 , CYS A:491 , HIS A:492 , HIS A:493 , ASN A:494 , PRO A:502 , LYS A:503 , CYS A:504 , CYS A:507 , HIS A:508 , ASP A:518 , PRO A:520 , ALA A:525 , GLN A:528 , GLN A:529 , HOH A:1328 , HOH A:1329
BINDING SITE FOR RESIDUE HEM A 1314
23
CC5
SOFTWARE
LEU A:458 , LYS A:462 , ILE A:463 , THR A:466 , LEU A:467 , GLN A:529 , CYS A:530 , CYS A:533 , HIS A:534 , LEU A:539 , GLU A:549 , CYS A:550 , HEM A:1313 , HOH A:1380 , HOH A:1472
BINDING SITE FOR RESIDUE HEM A 1315
24
CC6
SOFTWARE
ALA A:422 , ILE A:446 , GLY A:447 , VAL A:448 , LEU A:449 , SER A:450 , ASP A:451 , LYS A:452 , TYR A:453 , SER A:456 , LYS A:523 , TYR A:526 , HIS A:527 , CYS A:530 , MET A:531 , CYS A:547 , CYS A:550 , HIS A:551 , HOH A:1502
BINDING SITE FOR RESIDUE HEM A 1316
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2e84a_ (A:)
View:
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Classes
(
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(
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Folds
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(
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Superfamilies
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(
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Families
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Multiheme cytochromes
(149)
Superfamily
:
Multiheme cytochromes
(149)
Family
:
Cytochrome c3-like
(70)
Protein domain
:
automated matches
(17)
Desulfovibrio vulgaris [TaxId: 883]
(1)
1a
d2e84a_
A:
[
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]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2e84A02 (A:152-263)
1b: CATH_2e84A01 (A:32-151)
1c: CATH_2e84A04 (A:432-555)
1d: CATH_2e84A03 (A:275-431)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Cytochrome C3
(62)
Homologous Superfamily
:
Cytochrome C3
(62)
'miyazaki f' (Desulfovibrio vulgaris str)
(11)
1a
2e84A02
A:152-263
1b
2e84A01
A:32-151
1c
2e84A04
A:432-555
1d
2e84A03
A:275-431
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Protein & NOT Site
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